Contacts of the strand formed by residues 553 - 558 (chain E) in PDB entry 5MQF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 553 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510E TYR* 5.9 3.5 - - - +
511E ALA 5.5 0.3 - - - +
512E CYS* 4.6 8.3 - - - +
526E GLY* 4.2 9.2 - - - -
527E ASP 3.4 33.9 + - - +
528E GLY* 4.7 1.6 + - - -
530E GLY* 3.4 20.3 - - - +
531E LYS 4.4 1.1 - - - +
549E HIS* 5.2 1.6 - - + -
551E LYS 3.3 4.0 + - - -
552E VAL* 1.3 71.6 - - - +
554E ILE* 1.3 64.4 + - - +
555E GLY 4.7 1.6 - - - +
570E GLY 4.4 4.9 - - - +
571E TRP* 3.8 10.1 - - + -
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Residues in contact with ILE 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E VAL* 4.7 19.1 - - + +
511E ALA 3.7 6.7 - - - +
512E CYS* 3.2 11.8 - - - -
513E GLN* 3.2 16.3 + - - +
552E VAL 3.3 0.8 + - - -
553E CYS* 1.3 73.7 - - - +
555E GLY* 1.3 58.2 + - - +
570E GLY 3.0 7.4 + - - +
571E TRP* 3.2 28.7 - - - +
572E ASP* 4.2 3.4 - - + +
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Residues in contact with GLY 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512E CYS* 4.5 2.9 - - - -
513E GLN* 3.6 22.2 - - - -
526E GLY* 5.0 8.5 - - - -
553E CYS* 3.5 3.3 - - - +
554E ILE* 1.3 80.7 - - - +
556E ALA* 1.3 63.4 + - - +
569E CYS* 3.8 1.7 - - - +
570E GLY* 2.8 28.8 + - - +
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Residues in contact with ALA 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E VAL* 6.2 2.5 - - - -
513E GLN* 3.3 17.6 + - - +
514E VAL 3.7 17.5 - - - +
515E ASP* 3.7 20.0 - - + -
524E ILE* 4.7 3.6 - - + +
525E SER* 4.9 0.9 - - - -
526E GLY* 4.9 8.5 - - - +
555E GLY* 1.3 77.0 - - - +
557E VAL* 1.3 61.5 + - - +
567E ILE* 6.0 0.9 - - + -
568E THR 3.4 14.6 - - - +
569E CYS* 4.0 8.5 - - + +
570E GLY 4.5 0.2 - - - +
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Residues in contact with VAL 557 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E VAL* 5.9 6.7 - - + -
514E VAL 5.5 0.2 - - - -
515E ASP* 4.4 8.1 - - - +
556E ALA* 1.3 75.0 - - - +
558E TRP* 1.3 65.2 + - - +
567E ILE* 3.3 8.5 - - - +
568E THR* 2.9 42.5 + - - +
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Residues in contact with TRP 558 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515E ASP* 5.0 0.8 - - - +
516E PHE 3.3 31.0 - - - +
518E PRO* 4.8 7.4 - - + -
557E VAL* 1.3 79.2 - - - +
559E HIS* 1.3 69.8 + - - +
566E VAL 4.1 7.4 - - - +
567E ILE* 4.2 4.7 - - + +
568E THR* 5.2 1.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il